Face effects comparisons

In this script we will look at some interactive plots showing the effect of sex on the face across populations. Remember to open the file in chrome.

Preliminaries

We will load the necessary libraries, and datasets

setwd('..')
path <- getwd()
setwd(paste(path, "/Results/MergedData", sep = ""))
load("MergedDat.RData")
setwd(paste(path, "/Results/FacePCA", sep = ""))
eigenvec <- read.csv("eigenvectors.csv", header=F)
eigenval <- read.csv("eigenvalues.csv", header=F)
means    <- read.csv("means.csv", header=F)
facets   <- read.csv("facets.csv", header=F)
setwd(paste(path, "/Results/FSD", sep = ""))
vectors <- read.csv("popvectors.csv")

Face plots

In this section we will see the interactive plots showing facial sexual dimorphism. To do that we need to transform the PCA vectors to the shape coordinates. Each vector (total, allometric and non-allometric) is multiplied by a constant to exaggerate the facial effects (in this case 2 and -2), multiplied by the matrix of eigenvectors, and then added the means for each landmark.

cols <- rep(paste(vectors$continent, vectors$type, sep="."), 2)
sex  <- c(rep("Male", 18), rep("Female", 18))
cols <- paste(cols, sex, sep = ".")
fsdcoords <- as.data.frame(matrix(0, ncol = length(cols), nrow = nrow(means)))
colnames(fsdcoords) <- cols

fsdcoords[,c(1:18)] <- apply(as.matrix(vectors[, 2:88] * -2) %*% t(as.matrix(eigenvec)), 1, 
                              function(x) x + t(means))
fsdcoords[,c(19:36)] <- apply(as.matrix(vectors[, 2:88] * 2) %*% t(as.matrix(eigenvec)), 1, 
                              function(x) x + t(means))

averagecoords <- t(( rep(0, 87) %*% t(as.matrix(eigenvec))) + t(means))

source("PlotFaces.R")
Plot2Faces(fsdcoords[ ,1], fsdcoords[,19], facets, "AFR Total SD")

## Loading required package: plotly

## Loading required package: ggplot2

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

Plot2Faces(fsdcoords[ ,2], fsdcoords[,20], facets, "AMR Total SD")

Plot2Faces(fsdcoords[ ,3], fsdcoords[,21], facets, "EAS Total SD")

Plot2Faces(fsdcoords[ ,4], fsdcoords[,22], facets, "SAS Total SD")

Plot2Faces(fsdcoords[ ,5], fsdcoords[,23], facets, "NEU Total SD")

Plot2Faces(fsdcoords[ ,6], fsdcoords[,24], facets, "SEU Total SD")